Elhanan Borenstein, Ph.D.
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| NetCooperate>Examples |
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Here we provide some example networks that can be used to try out NetCooperate.
The example networks are available to download as tab-separated text files.
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Example 1: A pair of simple networks.
In this example, we have a pair of simple networks. The top network has two seed groups, one of size one and the other size three (circled with a double line). The bottom network has three seed groups, two singletons, and one two-node seed group (circled with a double line).
Seeds of one network present in the other are circled (solid lines: present, but not a seed of, the second network; dashed lines: present as a seed of the second network).
The Biosynthetic Support Score of the top network on the bottom (i.e. treating the top as a parasite of the bottom) is 1.0.
Note that all seed groups (but not all seeds) are present in the bottom network, and that node F is a seed of both networks.
The Metabolic Complementarity Index of the top network on the bottom (i.e. treating both networks as co-occurring microbes) is 0.5.
Because node F is a seed of the bottom network, it is not complementary to the top network’s seed set.
Download the example as a pair of text files here and here.
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Buchnera aphidicola
Acyrthosiphon pisum (pea aphid)
In this example, we present a host-endocytobiont pair.
The seed set of the metabolic network of B. Aphidicola was previously published in Borenstein et al. (2008) (supplement).
The metabolic network and seed set of A. pisum was generated using the same approach.
The BSS of B. aphidicola on A. pisum is 0.41667, which reflects the role of B. aphidicola as an obligate endocytobiont of A. pisum in this mutualistic interaction (Borenstein & Feldman 2009).
Only the giant components are considered here.
Download the example as a pair of text files here and here.
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